Literature DB >> 19279067

CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes.

Micah Hamady1, Stephanie A Wilson, Jesse Zaneveld, Noboru Sueoka, Rob Knight.   

Abstract

DNA composition in general, and codon usage in particular, is crucial for understanding gene function and evolution. CodonExplorer, available online at http://bmf.colorado.edu/codonexplorer/, is an online tool and interactive database that contains millions of genes, allowing rapid exploration of the factors governing gene and genome compositional evolution and exploiting GC content and codon usage frequency to identify genes with composition suggesting high levels of expression or horizontal transfer.

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Year:  2009        PMID： 19279067      PMCID： PMC2677738          DOI： 10.1093/bioinformatics/btp141

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  11 in total

1.  Wide intra-genomic G+C heterogeneity in human and chicken is mainly due to strand-symmetric directional mutation pressures: dGTP-oxidation and symmetric cytosine-deamination hypotheses.

Authors:  Noboru Sueoka
Journal:  Gene       Date:  2002-10-30       Impact factor: 3.688

2.  Compositional correlation between deoxyribonucleic acid and protein.

Authors:  N SUEOKA
Journal:  Cold Spring Harb Symp Quant Biol       Date:  1961

3.  The guanine and cytosine content of genomic DNA and bacterial evolution.

Authors:  A Muto; S Osawa
Journal:  Proc Natl Acad Sci U S A       Date:  1987-01       Impact factor: 11.205

4.  The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

Authors:  P M Sharp; W H Li
Journal:  Nucleic Acids Res       Date:  1987-02-11       Impact factor: 16.971

5.  Intrastrand parity rules of DNA base composition and usage biases of synonymous codons.

Authors:  N Sueoka
Journal:  J Mol Evol       Date:  1995-03       Impact factor: 2.395

6.  Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa.

Authors:  S K Gupta; T C Ghosh
Journal:  Gene       Date:  2001-07-25       Impact factor: 3.688

Review 7.  The vertebrate genome: isochores and evolution.

Authors:  G Bernardi
Journal:  Mol Biol Evol       Date:  1993-01       Impact factor: 16.240

8.  Codon usages in different gene classes of the Escherichia coli genome.

Authors:  S Karlin; J Mrázek; A M Campbell
Journal:  Mol Microbiol       Date:  1998-09       Impact factor: 3.501

9.  Asymmetric directional mutation pressures in bacteria.

Authors:  Jean R Lobry; Noboru Sueoka
Journal:  Genome Biol       Date:  2002-09-26       Impact factor: 13.583

10.  PyCogent: a toolkit for making sense from sequence.

Authors:  Rob Knight; Peter Maxwell; Amanda Birmingham; Jason Carnes; J Gregory Caporaso; Brett C Easton; Michael Eaton; Micah Hamady; Helen Lindsay; Zongzhi Liu; Catherine Lozupone; Daniel McDonald; Michael Robeson; Raymond Sammut; Sandra Smit; Matthew J Wakefield; Jeremy Widmann; Shandy Wikman; Stephanie Wilson; Hua Ying; Gavin A Huttley
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583
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  1 in total

1.  CBDB: the codon bias database.

Authors:  Adam Hilterbrand; Joseph Saelens; Catherine Putonti
Journal:  BMC Bioinformatics       Date:  2012-04-26       Impact factor: 3.169
  1 in total

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